9 |
|
#include <sys/stat.h> |
10 |
|
|
11 |
|
#include "ReadWrite.hpp" |
12 |
+ |
#include "simError.h" |
13 |
|
|
14 |
|
|
15 |
|
InitializeFromFile :: InitializeFromFile( char *in_name ){ |
16 |
+ |
#ifdef IS_MPI |
17 |
+ |
if (worldRank == 0) { |
18 |
+ |
#endif |
19 |
|
|
20 |
|
c_in_file = fopen(in_name, "r"); |
21 |
|
if(c_in_file == NULL){ |
22 |
< |
printf("Cannot open file: %s\n", in_name); |
23 |
< |
exit(8); |
22 |
> |
sprintf(painCave.errMsg, |
23 |
> |
"Cannot open file: %s\n", in_name); |
24 |
> |
painCave.isFatal = 1; |
25 |
> |
simError(); |
26 |
|
} |
27 |
|
|
28 |
|
strcpy( c_in_name, in_name); |
29 |
+ |
#ifdef IS_MPI |
30 |
+ |
} |
31 |
+ |
strcpy( checkPointMsg, "Infile opened for reading successfully." ); |
32 |
+ |
MPIcheckPoint(); |
33 |
+ |
#endif |
34 |
|
return; |
35 |
|
} |
36 |
|
|
37 |
|
InitializeFromFile :: ~InitializeFromFile( ){ |
38 |
< |
|
38 |
> |
#ifdef IS_MPI |
39 |
> |
if (worldRank == 0) { |
40 |
> |
#endif |
41 |
|
int error; |
42 |
|
error = fclose( c_in_file ); |
43 |
|
if( error ){ |
44 |
< |
fprintf( stderr, "Error closing %s\n", c_in_name ); |
44 |
> |
sprintf( painCave.errMsg, |
45 |
> |
"Error closing %s\n", c_in_name ); |
46 |
> |
simError(); |
47 |
|
} |
48 |
+ |
#ifdef IS_MPI |
49 |
+ |
} |
50 |
+ |
strcpy( checkPointMsg, "Infile closed successfully." ); |
51 |
+ |
MPIcheckPoint(); |
52 |
+ |
#endif |
53 |
+ |
|
54 |
|
return; |
55 |
|
} |
56 |
|
|
57 |
|
|
58 |
< |
void InitializeFromFile :: read_xyz( SimInfo* entry_plug ){ |
58 |
> |
void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
59 |
|
|
60 |
|
int i; // loop counter |
61 |
|
|
62 |
+ |
const int BUFFERSIZE = 2000; // size of the read buffer |
63 |
|
int n_atoms; // the number of atoms |
64 |
< |
char read_buffer[2000]; //the line buffer for reading |
64 |
> |
char read_buffer[BUFFERSIZE]; //the line buffer for reading |
65 |
> |
#ifdef IS_MPI |
66 |
> |
char send_buffer[BUFFERSIZE]; |
67 |
> |
#endif |
68 |
> |
|
69 |
|
char *eof_test; // ptr to see when we reach the end of the file |
70 |
< |
char *foo; // the pointer to the current string token |
70 |
> |
char *parseErr; |
71 |
|
|
46 |
– |
double rx, ry, rz; // position place holders |
47 |
– |
double vx, vy, vz; // velocity placeholders |
48 |
– |
double q[4]; // the quaternions |
49 |
– |
double jx, jy, jz; // angular velocity placeholders; |
50 |
– |
double qSqr, qLength; // needed to normalize the quaternion vector. |
72 |
|
|
73 |
+ |
entry_plug = the_entry_plug |
74 |
+ |
|
75 |
+ |
|
76 |
+ |
#ifndef IS_MPI |
77 |
|
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
78 |
|
if( eof_test == NULL ){ |
79 |
< |
std::cerr << "error reading 1st line of" << c_in_name << "\n"; |
79 |
> |
sprintf( painCave.errMsg, |
80 |
> |
"InitializeFromFile error: error reading 1st line of \"%s\"\n", |
81 |
> |
c_in_name ); |
82 |
> |
painCave.isFatal = 1; |
83 |
> |
simError(); |
84 |
|
} |
85 |
|
|
86 |
< |
(void)sscanf(read_buffer, "%d", &n_atoms); |
86 |
> |
n_atoms = atoi( read_buffer ); |
87 |
|
|
88 |
|
Atom **atoms = entry_plug->atoms; |
89 |
|
DirectionalAtom* dAtom; |
90 |
|
|
91 |
|
if( n_atoms != entry_plug->n_atoms ){ |
92 |
< |
fprintf( stderr, |
92 |
> |
sprintf( painCave.errMsg, |
93 |
|
"Initialize from File error. %s n_atoms, %d, " |
94 |
|
"does not match the BASS file's n_atoms, %d.\n", |
95 |
|
c_in_name, n_atoms, entry_plug->n_atoms ); |
96 |
< |
exit(8); |
96 |
> |
painCave.isFatal = 1; |
97 |
> |
simError(); |
98 |
|
} |
99 |
|
|
100 |
|
//read and toss the comment line |
101 |
|
|
102 |
|
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
103 |
|
if(eof_test == NULL){ |
104 |
< |
printf("error in reading commment in %s\n", c_in_name); |
105 |
< |
exit(8); |
104 |
> |
sprintf( painCave.errMsg, |
105 |
> |
"error in reading commment in %s\n", c_in_name); |
106 |
> |
painCave.isFatal = 1; |
107 |
> |
simError(); |
108 |
|
} |
109 |
|
|
110 |
|
for( i=0; i < n_atoms; i++){ |
111 |
|
|
112 |
|
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
113 |
|
if(eof_test == NULL){ |
114 |
< |
printf("error in reading file %s\n" |
115 |
< |
"natoms = %d; index = %d\n" |
116 |
< |
"error reading the line from the file.\n", |
117 |
< |
c_in_name, n_atoms, i ); |
118 |
< |
exit(8); |
114 |
> |
sprintf(painCave.errMsg, |
115 |
> |
"error in reading file %s\n" |
116 |
> |
"natoms = %d; index = %d\n" |
117 |
> |
"error reading the line from the file.\n", |
118 |
> |
c_in_name, n_atoms, i ); |
119 |
> |
painCave.isFatal = 1; |
120 |
> |
simError(); |
121 |
|
} |
122 |
|
|
89 |
– |
foo = strtok(read_buffer, " ,;\t"); |
123 |
|
|
124 |
< |
// check the atom name to the current atom |
124 |
> |
parseErr = parseDumpLine( read_buffer, i ); |
125 |
> |
if( parseErr != NULL ){ |
126 |
> |
strcpy( painCave.errMsg, parseErr ); |
127 |
> |
painCave.isFatal = 1; |
128 |
> |
simError(); |
129 |
> |
} |
130 |
> |
} |
131 |
|
|
132 |
< |
if( strcmp( foo, atoms[i]->getType() ) ){ |
133 |
< |
fprintf( stderr, |
134 |
< |
"Initialize from file error. Atom %s at index %d " |
135 |
< |
"in file %s does not" |
136 |
< |
" match the BASS atom %s.\n", |
137 |
< |
foo, i, c_in_name, atoms[i]->getType() ); |
138 |
< |
exit(8); |
132 |
> |
|
133 |
> |
// MPI Section of code.......... |
134 |
> |
#else //IS_MPI |
135 |
> |
|
136 |
> |
|
137 |
> |
|
138 |
> |
|
139 |
> |
if (worldRank == 0) { |
140 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
141 |
> |
if( eof_test == NULL ){ |
142 |
> |
sprintf( painCave.errMsg, |
143 |
> |
"Error reading 1st line of %d \n ",c_in_name); |
144 |
> |
painCave.isFatal = 1; |
145 |
> |
simError(); |
146 |
|
} |
147 |
|
|
148 |
< |
// get the positions |
149 |
< |
|
150 |
< |
foo = strtok(NULL, " ,;\t"); |
151 |
< |
if(foo == NULL){ |
152 |
< |
printf("error in reading postition x from %s\n" |
153 |
< |
"natoms = %d, index = %d\n", |
154 |
< |
c_in_name, n_atoms, i ); |
155 |
< |
exit(8); |
148 |
> |
n_atoms = atoi( read_buffer ); |
149 |
> |
|
150 |
> |
Atom **atoms = entry_plug->atoms; |
151 |
> |
DirectionalAtom* dAtom; |
152 |
> |
|
153 |
> |
if( n_atoms != entry_plug->mpiSim->getTotAtoms() ){ |
154 |
> |
sprintf( painCave.errMsg, |
155 |
> |
"Initialize from File error. %s n_atoms, %d, " |
156 |
> |
"does not match the BASS file's n_atoms, %d.\n", |
157 |
> |
c_in_name, n_atoms, entry_plug->n_atoms ); |
158 |
> |
painCave.isFatal = 1; |
159 |
> |
simError(); |
160 |
|
} |
161 |
< |
(void)sscanf( foo, "%lf", &rx ); |
162 |
< |
|
163 |
< |
foo = strtok(NULL, " ,;\t"); |
164 |
< |
if(foo == NULL){ |
165 |
< |
printf("error in reading postition y from %s\n" |
166 |
< |
"natoms = %d, index = %d\n", |
167 |
< |
c_in_name, n_atoms, i ); |
168 |
< |
exit(8); |
161 |
> |
|
162 |
> |
//read and toss the comment line |
163 |
> |
|
164 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
165 |
> |
if(eof_test == NULL){ |
166 |
> |
sprintf( painCave.errMsg, |
167 |
> |
"error in reading commment in %s\n", c_in_name); |
168 |
> |
painCave.isFatal = 1; |
169 |
> |
simError(); |
170 |
|
} |
171 |
< |
(void)sscanf( foo, "%lf", &ry ); |
172 |
< |
|
173 |
< |
foo = strtok(NULL, " ,;\t"); |
174 |
< |
if(foo == NULL){ |
175 |
< |
printf("error in reading postition z from %s\n" |
176 |
< |
"natoms = %d, index = %d\n", |
177 |
< |
c_in_name, n_atoms, i ); |
178 |
< |
exit(8); |
171 |
> |
} |
172 |
> |
|
173 |
> |
for( i=0; i < n_atoms; i++){ |
174 |
> |
|
175 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
176 |
> |
if(eof_test == NULL){ |
177 |
> |
sprintf(painCave.errMsg, |
178 |
> |
"error in reading file %s\n" |
179 |
> |
"natoms = %d; index = %d\n" |
180 |
> |
"error reading the line from the file.\n", |
181 |
> |
c_in_name, n_atoms, i ); |
182 |
> |
painCave.isFatal = 1; |
183 |
> |
simError(); |
184 |
|
} |
129 |
– |
(void)sscanf( foo, "%lf", &rz ); |
185 |
|
|
186 |
< |
// get the velocities |
186 |
> |
parseErr = parseDumpLine( read_buffer, i ); |
187 |
> |
if( parseErr != NULL ){ |
188 |
> |
strcpy( painCave.errMsg, parseErr ); |
189 |
> |
painCave.isFatal = 1; |
190 |
> |
simError(); |
191 |
> |
} |
192 |
> |
} |
193 |
> |
#endif |
194 |
> |
} |
195 |
|
|
196 |
< |
foo = strtok(NULL, " ,;\t"); |
197 |
< |
if(foo == NULL){ |
198 |
< |
printf("error in reading velocity x from %s\n" |
199 |
< |
"natoms = %d, index = %d\n", |
200 |
< |
c_in_name, n_atoms, i ); |
201 |
< |
exit(8); |
202 |
< |
} |
203 |
< |
(void)sscanf( foo, "%lf", &vx ); |
196 |
> |
|
197 |
> |
char* IntitializeFromFile::parseDumpLine(char* readLine, int atomIndex){ |
198 |
> |
|
199 |
> |
char *foo; // the pointer to the current string token |
200 |
> |
|
201 |
> |
double rx, ry, rz; // position place holders |
202 |
> |
double vx, vy, vz; // velocity placeholders |
203 |
> |
double q[4]; // the quaternions |
204 |
> |
double jx, jy, jz; // angular velocity placeholders; |
205 |
> |
double qSqr, qLength; // needed to normalize the quaternion vector. |
206 |
> |
|
207 |
> |
Atom **atoms = entry_plug->atoms; |
208 |
> |
DirectionalAtom* dAtom; |
209 |
> |
|
210 |
> |
int n_atoms; |
211 |
> |
|
212 |
> |
#ifdef IS_MPI |
213 |
> |
n_atoms = entry_plug->mpiSim->getTotAtoms(); |
214 |
> |
#else |
215 |
> |
n_atoms = entry_plug->n_atoms; |
216 |
> |
#endi // is_mpi |
217 |
> |
|
218 |
> |
|
219 |
> |
// set the string tokenizer |
220 |
> |
|
221 |
> |
foo = strtok(readLine, " ,;\t"); |
222 |
> |
|
223 |
> |
// check the atom name to the current atom |
224 |
> |
|
225 |
> |
if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
226 |
> |
sprintf( painCave.errMsg, |
227 |
> |
"Initialize from file error. Atom %s at index %d " |
228 |
> |
"in file %s does not" |
229 |
> |
" match the BASS atom %s.\n", |
230 |
> |
foo, atomIndex, c_in_name, atoms[atomIndex]->getType() ); |
231 |
> |
return strdup( painCave.errMsg ); |
232 |
> |
} |
233 |
|
|
234 |
< |
foo = strtok(NULL, " ,;\t"); |
235 |
< |
if(foo == NULL){ |
236 |
< |
printf("error in reading velocity y from %s\n" |
234 |
> |
// get the positions |
235 |
> |
|
236 |
> |
foo = strtok(NULL, " ,;\t"); |
237 |
> |
if(foo == NULL){ |
238 |
> |
sprintf( painCave.errMsg, |
239 |
> |
"error in reading postition x from %s\n" |
240 |
|
"natoms = %d, index = %d\n", |
241 |
< |
c_in_name, n_atoms, i ); |
242 |
< |
exit(8); |
243 |
< |
} |
244 |
< |
(void)sscanf( foo, "%lf", &vy ); |
245 |
< |
|
246 |
< |
foo = strtok(NULL, " ,;\t"); |
247 |
< |
if(foo == NULL){ |
248 |
< |
printf("error in reading velocity z from %s\n" |
241 |
> |
c_in_name, n_atoms, atomIndex ); |
242 |
> |
return strdup( painCave.errMsg ); |
243 |
> |
} |
244 |
> |
rx = atof( foo ); |
245 |
> |
|
246 |
> |
foo = strtok(NULL, " ,;\t"); |
247 |
> |
if(foo == NULL){ |
248 |
> |
sprintf( painCave.errMsg, |
249 |
> |
"error in reading postition y from %s\n" |
250 |
|
"natoms = %d, index = %d\n", |
251 |
< |
c_in_name, n_atoms, i ); |
252 |
< |
exit(8); |
253 |
< |
} |
254 |
< |
(void)sscanf( foo, "%lf", &vz ); |
251 |
> |
c_in_name, n_atoms, atomIndex ); |
252 |
> |
return strdup( painCave.errMsg ); |
253 |
> |
} |
254 |
> |
ry = atof( foo ); |
255 |
> |
|
256 |
> |
foo = strtok(NULL, " ,;\t"); |
257 |
> |
if(foo == NULL){ |
258 |
> |
sprintf( painCave.errMsg, |
259 |
> |
"error in reading postition z from %s\n" |
260 |
> |
"natoms = %d, index = %d\n", |
261 |
> |
c_in_name, n_atoms, atomIndex ); |
262 |
> |
return strdup( painCave.errMsg ); |
263 |
> |
} |
264 |
> |
rz = atof( foo ); |
265 |
> |
|
266 |
> |
|
267 |
> |
// get the velocities |
268 |
> |
|
269 |
> |
foo = strtok(NULL, " ,;\t"); |
270 |
> |
if(foo == NULL){ |
271 |
> |
sprintf( painCave.errMsg, |
272 |
> |
"error in reading velocity x from %s\n" |
273 |
> |
"natoms = %d, index = %d\n", |
274 |
> |
c_in_name, n_atoms, atomIndex ); |
275 |
> |
return strdup( painCave.errMsg ); |
276 |
> |
} |
277 |
> |
vx = atof( foo ); |
278 |
|
|
279 |
+ |
foo = strtok(NULL, " ,;\t"); |
280 |
+ |
if(foo == NULL){ |
281 |
+ |
sprintf( painCave.errMsg, |
282 |
+ |
"error in reading velocity y from %s\n" |
283 |
+ |
"natoms = %d, index = %d\n", |
284 |
+ |
c_in_name, n_atoms, atomIndex ); |
285 |
+ |
return strdup( painCave.errMsg ); |
286 |
+ |
} |
287 |
+ |
vy = atof( foo ); |
288 |
|
|
289 |
< |
// get the quaternions |
289 |
> |
foo = strtok(NULL, " ,;\t"); |
290 |
> |
if(foo == NULL){ |
291 |
> |
sprintf( painCave.errMsg, |
292 |
> |
"error in reading velocity z from %s\n" |
293 |
> |
"natoms = %d, index = %d\n", |
294 |
> |
c_in_name, n_atoms, atomIndex ); |
295 |
> |
return strdup( painCave.errMsg ); |
296 |
> |
} |
297 |
> |
vz = atof( foo ); |
298 |
|
|
299 |
< |
if( atoms[i]->isDirectional() ){ |
299 |
> |
|
300 |
> |
// get the quaternions |
301 |
> |
|
302 |
> |
if( atoms[atomIndex]->isDirectional() ){ |
303 |
|
|
304 |
< |
foo = strtok(NULL, " ,;\t"); |
305 |
< |
if(foo == NULL){ |
306 |
< |
printf("error in reading quaternion 0 from %s\n" |
304 |
> |
foo = strtok(NULL, " ,;\t"); |
305 |
> |
if(foo == NULL){ |
306 |
> |
sprintf(painCave.errMsg, |
307 |
> |
"error in reading quaternion 0 from %s\n" |
308 |
> |
"natoms = %d, index = %d\n", |
309 |
> |
c_in_name, n_atoms, atomIndex ); |
310 |
> |
return strdup( painCave.errMsg ); |
311 |
> |
} |
312 |
> |
q[0] = atof( foo ); |
313 |
> |
|
314 |
> |
foo = strtok(NULL, " ,;\t"); |
315 |
> |
if(foo == NULL){ |
316 |
> |
sprintf( painCave.errMsg, |
317 |
> |
"error in reading quaternion 1 from %s\n" |
318 |
|
"natoms = %d, index = %d\n", |
319 |
< |
c_in_name, n_atoms, i ); |
320 |
< |
exit(8); |
321 |
< |
} |
322 |
< |
(void)sscanf( foo, "%lf", &q[0] ); |
319 |
> |
c_in_name, n_atoms, atomIndex ); |
320 |
> |
return strdup( painCave.errMsg ); |
321 |
> |
} |
322 |
> |
q[1] = atof( foo ); |
323 |
|
|
324 |
< |
foo = strtok(NULL, " ,;\t"); |
325 |
< |
if(foo == NULL){ |
326 |
< |
printf("error in reading quaternion 1 from %s\n" |
324 |
> |
foo = strtok(NULL, " ,;\t"); |
325 |
> |
if(foo == NULL){ |
326 |
> |
sprintf( painCave.errMsg, |
327 |
> |
"error in reading quaternion 2 from %s\n" |
328 |
|
"natoms = %d, index = %d\n", |
329 |
< |
c_in_name, n_atoms, i ); |
330 |
< |
exit(8); |
331 |
< |
} |
332 |
< |
(void)sscanf( foo, "%lf", &q[1] ); |
329 |
> |
c_in_name, n_atoms, atomIndex ); |
330 |
> |
return strdup( painCave.errMsg ); |
331 |
> |
} |
332 |
> |
q[2] = atof( foo ); |
333 |
|
|
334 |
< |
foo = strtok(NULL, " ,;\t"); |
335 |
< |
if(foo == NULL){ |
336 |
< |
printf("error in reading quaternion 2 from %s\n" |
334 |
> |
foo = strtok(NULL, " ,;\t"); |
335 |
> |
if(foo == NULL){ |
336 |
> |
sprintf( painCave.errMsg, |
337 |
> |
"error in reading quaternion 3 from %s\n" |
338 |
|
"natoms = %d, index = %d\n", |
339 |
< |
c_in_name, n_atoms, i ); |
340 |
< |
exit(8); |
341 |
< |
} |
342 |
< |
(void)sscanf( foo, "%lf", &q[2] ); |
191 |
< |
|
192 |
< |
foo = strtok(NULL, " ,;\t"); |
193 |
< |
if(foo == NULL){ |
194 |
< |
printf("error in reading quaternion 3 from %s\n" |
195 |
< |
"natoms = %d, index = %d\n", |
196 |
< |
c_in_name, n_atoms, i ); |
197 |
< |
exit(8); |
198 |
< |
} |
199 |
< |
(void)sscanf( foo, "%lf", &q[3] ); |
339 |
> |
c_in_name, n_atoms, atomIndex ); |
340 |
> |
return strdup( painCave.errMsg ); |
341 |
> |
} |
342 |
> |
q[3] = atof( foo ); |
343 |
|
|
344 |
< |
// get the angular velocities |
344 |
> |
// get the angular velocities |
345 |
|
|
346 |
< |
foo = strtok(NULL, " ,;\t"); |
347 |
< |
if(foo == NULL){ |
348 |
< |
printf("error in reading angular momentum jx from %s\n" |
346 |
> |
foo = strtok(NULL, " ,;\t"); |
347 |
> |
if(foo == NULL){ |
348 |
> |
sprintf( painCave.errMsg, |
349 |
> |
"error in reading angular momentum jx from %s\n" |
350 |
|
"natoms = %d, index = %d\n", |
351 |
< |
c_in_name, n_atoms, i ); |
352 |
< |
exit(8); |
353 |
< |
} |
354 |
< |
(void)sscanf( foo, "%lf", &jx ); |
351 |
> |
c_in_name, n_atoms, atomIndex ); |
352 |
> |
return strdup( painCave.errMsg ); |
353 |
> |
} |
354 |
> |
jx = atof( foo ); |
355 |
|
|
356 |
< |
foo = strtok(NULL, " ,;\t"); |
357 |
< |
if(foo == NULL){ |
358 |
< |
printf("error in reading angular momentum jy from %s\n" |
356 |
> |
foo = strtok(NULL, " ,;\t"); |
357 |
> |
if(foo == NULL){ |
358 |
> |
sprintf( painCave.errMsg, |
359 |
> |
"error in reading angular momentum jy from %s\n" |
360 |
|
"natoms = %d, index = %d\n", |
361 |
< |
c_in_name, n_atoms, i ); |
362 |
< |
exit(8); |
363 |
< |
} |
364 |
< |
(void)sscanf( foo, "%lf", &jy ); |
361 |
> |
c_in_name, n_atoms, atomIndex ); |
362 |
> |
return strdup( painCave.errMsg ); |
363 |
> |
} |
364 |
> |
jy = atof(foo ); |
365 |
|
|
366 |
< |
foo = strtok(NULL, " ,;\t"); |
367 |
< |
if(foo == NULL){ |
368 |
< |
printf("error in reading angular momentum jz from %s\n" |
366 |
> |
foo = strtok(NULL, " ,;\t"); |
367 |
> |
if(foo == NULL){ |
368 |
> |
sprintf( painCave.errMsg, |
369 |
> |
"error in reading angular momentum jz from %s\n" |
370 |
|
"natoms = %d, index = %d\n", |
371 |
< |
c_in_name, n_atoms, i ); |
372 |
< |
exit(8); |
373 |
< |
} |
374 |
< |
(void)sscanf( foo, "%lf", &jz ); |
371 |
> |
c_in_name, n_atoms, atomIndex ); |
372 |
> |
return strdup( painCave.errMsg ); |
373 |
> |
} |
374 |
> |
jz = atof( foo ); |
375 |
|
|
376 |
< |
dAtom = ( DirectionalAtom* )atoms[i]; |
376 |
> |
dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
377 |
|
|
378 |
< |
// check that the quaternion vector is normalized |
378 |
> |
// check that the quaternion vector is normalized |
379 |
|
|
380 |
< |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
380 |
> |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
381 |
|
|
382 |
< |
qLength = sqrt( qSqr ); |
383 |
< |
q[0] = q[0] / qLength; |
384 |
< |
q[1] = q[1] / qLength; |
385 |
< |
q[2] = q[2] / qLength; |
386 |
< |
q[3] = q[3] / qLength; |
382 |
> |
qLength = sqrt( qSqr ); |
383 |
> |
q[0] = q[0] / qLength; |
384 |
> |
q[1] = q[1] / qLength; |
385 |
> |
q[2] = q[2] / qLength; |
386 |
> |
q[3] = q[3] / qLength; |
387 |
|
|
388 |
< |
dAtom->setQ( q ); |
388 |
> |
dAtom->setQ( q ); |
389 |
|
|
390 |
< |
// add the angular velocities |
390 |
> |
// add the angular velocities |
391 |
|
|
392 |
< |
dAtom->setJx( jx ); |
393 |
< |
dAtom->setJy( jy ); |
394 |
< |
dAtom->setJz( jz ); |
395 |
< |
} |
392 |
> |
dAtom->setJx( jx ); |
393 |
> |
dAtom->setJy( jy ); |
394 |
> |
dAtom->setJz( jz ); |
395 |
> |
} |
396 |
|
|
397 |
< |
// add the positions and velocities to the atom |
397 |
> |
// add the positions and velocities to the atom |
398 |
|
|
399 |
< |
atoms[i]->setX( rx ); |
400 |
< |
atoms[i]->setY( ry ); |
401 |
< |
atoms[i]->setZ( rz ); |
399 |
> |
atoms[atomIndex]->setX( rx ); |
400 |
> |
atoms[atomIndex]->setY( ry ); |
401 |
> |
atoms[atomIndex]->setZ( rz ); |
402 |
|
|
403 |
< |
atoms[i]->set_vx( vx ); |
404 |
< |
atoms[i]->set_vy( vy ); |
405 |
< |
atoms[i]->set_vz( vz ); |
406 |
< |
|
407 |
< |
} |
403 |
> |
atoms[atomIndex]->set_vx( vx ); |
404 |
> |
atoms[atomIndex]->set_vy( vy ); |
405 |
> |
atoms[atomIndex]->set_vz( vz ); |
406 |
> |
|
407 |
> |
return NULL; |
408 |
|
} |